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The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine–cytosine base pairs in Watson–Crick and Hoogsteen configurations

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Abstract

The theoretical IR and Raman spectra of the guanine–cytosine DNA base pairs in Watson–Crick and Hoogsteen configurations were computed using DFT method with M06-2X meta-hybrid GGA exchange-correlation functional, including the anharmonic corrections and solvent effects. The results for harmonic frequencies and their anharmonic corrections were compared with our previously calculated values obtained with the B3PW91 hybrid GGA functional. Significant differences were obtained for the anharmonic corrections calculated with the two different DFT functionals, especially for the stretching modes, while the corresponding harmonic frequencies did not differ considerable. For the Hoogtseen case the H+ vibration between the G-C base pair can be characterized as an asymmetric Duffing oscillator and therefore unrealistic anharmonic corrections for normal modes where this proton vibration is involved have been obtained. The spectral modification due to the anharmonic corrections, solvent effects and the influence of sugar-phosphate group for the Watson-Crick and Hoogsteen base pair configurations, respectively, were also discussed. For the Watson-Crick case also the influence of the stacking interaction on the theoretical IR and Raman spectra was analyzed. Including the anharmonic correction in our normal mode analysis is essential if one wants to obtain correct assignments of the theoretical frequency values as compared with the experimental spectra.

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Acknowledgments

This work was supported by a grant of the Ministry of National Education, National Authority for Scientific Research CNCS–UEFISCDI, Romania, project number PN-II-ID-PCE-2012-4-0115. Thanks are due to National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania Data Center for providing computer facilities.

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  1. Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Donath Street, No. 65-103, 400293, Cluj-Napoca, Romania

    Attila Bende & Cristina M. Muntean

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  1. Attila Bende
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Correspondence to Cristina M. Muntean.

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Bende, A., Muntean, C.M. The influence of anharmonic and solvent effects on the theoretical vibrational spectra of the guanine–cytosine base pairs in Watson–Crick and Hoogsteen configurations. J Mol Model 20, 2113 (2014). https://doi.org/10.1007/s00894-014-2113-z

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